# ClinicoPath 0.0.2.0016

- See: https://github.com/sbalci/jjstatsplot/releases/ - See: https://github.com/sbalci/ClinicoPath/releases/ - crosstable function partially resolves jamovi/jamovi#443 - survival function resolves jonathon-love/deathwatch#2 - added export html to crosstables to bypass jamovi/jamovi#892
sbalci · Jun 30, 2020 · 3f00938 · 3f00938
1 parent 3fe2f73
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diff --git a/.Rprofile b/.Rprofile
@@ -9,6 +9,26 @@ options(repos = c("https://cran.microsoft.com/snapshot/2020-05-01"))
 
 # .libPaths(new = "~/histopathRprojects/ClinicoPathLibrary")
 
+
+# options(repos = c("https://cran.microsoft.com/snapshot/2020-05-01"))
+
+# .libPaths(new = "C:\\ClinicoPathLibrary")
+
+# Sys.setenv(TZ = "Europe/Istanbul")
+
+# Sys.setenv(TEMP = "C:\\temp")
+
+# Sys.setenv(TMP = "C:\\temp")
+
+
+# jmvtools::check("C://Program Files//jamovi//bin")
+# jmvtools::install(home = "C://Program Files//jamovi//bin")
+#
+#
+#
+
+
+
 # source(
 #     "renv/activate.R"
 # "~/histopathRprojects/ClinicoPath/renv/activate.R"

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPath
 Title: Analysis for Clinicopathological Research
-Version: 0.0.2.0015
-Date: 2020-06-28
+Version: 0.0.2.0016
+Date: 2020-06-29
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,24 @@
+# ClinicoPath 0.0.2.0016
+
+- See: https://github.com/sbalci/jjstatsplot/releases/
+
+- See: https://github.com/sbalci/ClinicoPath/releases/
+
+- crosstable function partially resolves https://github.com/jamovi/jamovi/issues/443
+
+- survival function resolves https://github.com/jonathon-love/deathwatch/issues/2
+
+- added export html to crosstables to bypass https://github.com/jamovi/jamovi/issues/892
+
+
+
+
 # ClinicoPath 0.0.2.0015
 
 - Added tangram statistical results
 - Added options to finalfit crosstables
 fixes: https://github.com/sbalci/ClinicoPathJamoviModule/issues/24
-fixes: https://github.com/jamovi/jamovi/issues/901
+Partially fixes: https://github.com/jamovi/jamovi/issues/901
 fixes: https://github.com/ewenharrison/finalfit/issues/52
 
 - Added experimental biblometrics functions

diff --git a/R/00jmv.R b/R/00jmv.R
@@ -314,22 +314,23 @@
         `url`="https://CRAN.R-project.org/package=hrbrthemes"), 
     `retractcheck`=list(
         `type`="software", 
-        `author`=NULL, 
-        `year`=NULL, 
-        `title`="", 
-        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", 
-        `url`="https://CRAN.R-project.org/package="), 
+        `author`="Chris Hartgerink and Frederik Aust", 
+        `year`=2019, 
+        `title`="retractcheck: Retraction Scanner", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=retractcheck", 
+        `url`="https://CRAN.R-project.org/package=retractcheck"), 
     `RefManageR`=list(
         `type`="software", 
-        `author`=NULL, 
-        `year`=NULL, 
-        `title`="", 
-        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", 
-        `url`="https://CRAN.R-project.org/package="), 
+        `author`="McLean MW", 
+        `year`=2017, 
+        `title`="RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.", 
+        `doi`="10.21105/joss.00338", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=RefManageR", 
+        `url`="https://CRAN.R-project.org/package=RefManageR"), 
     `rcrossref`=list(
         `type`="software", 
-        `author`=NULL, 
-        `year`=NULL, 
-        `title`="", 
-        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", 
-        `url`="https://CRAN.R-project.org/package="))
+        `author`="Scott Chamberlain and Hao Zhu and Najko Jahn and Carl Boettiger and Karthik Ram", 
+        `year`=2020, 
+        `title`="rcrossref: Client for Various 'CrossRef' 'APIs'", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=rcrossref", 
+        `url`="https://CRAN.R-project.org/package=rcrossref"))
diff --git a/R/crosstable.b.R b/R/crosstable.b.R
@@ -268,10 +268,29 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
                 if (export)
                 {
+
+
+
+                    if (.Platform$OS.type == "windows") {
+
+                        stopifnot(file.exists("C:\\temp2"))
+
+                        write(
+                            x = tabletangram,
+                            file = "C:\\temp2\\ClinicoPathCrossTable.html"
+                        )
+
+
+                    } else {
+
+
                     write(x = tabletangram,
                           file = "~/Documents/ClinicoPathCrossTable.html"
-
                           )
+
+                    }
+
+
                 }
 
 

diff --git a/R/tree.b.R b/R/tree.b.R
@@ -85,7 +85,7 @@ treeClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
             tree <- rpart::rpart(myformula, data = mydata, cp = .02)
 
-            # self$results$text2$setContent(tree)
+            self$results$text2$setContent(tree)
 
 
             # FFTrees ----
@@ -113,7 +113,7 @@ treeClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
 
 
-                # self$results$text2$setContent(mydata)
+                self$results$text2$setContent(mydata)
 
 
             }
@@ -200,6 +200,7 @@ treeClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             myformula <- as.formula(myformula)
 
             # FFTrees ----
+            # https://ndphillips.github.io/useR2017_pres/#1
 
             mytree.fft <- FFTrees::FFTrees(
                 formula = myformula,
@@ -250,7 +251,9 @@ treeClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             myformula <- as.formula(myformula)
 
 
-            tree <- rpart::rpart(myformula, data = mydata, cp = .02)
+            tree <- rpart::rpart(myformula,
+                                 data = mydata,
+                                 cp = .02)
 
 
             plot3 <- rpart.plot::rpart.plot(tree,

diff --git a/README.Rmd b/README.Rmd
@@ -4,7 +4,7 @@ output: github_document
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-```{r, include = FALSE}
+```{r global options, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
@@ -64,17 +64,41 @@ Then you can install this module directly inside the jamovi, using library.
 ## Installation via sideload [jamovi](https://www.jamovi.org)
 
 
-- Step 1: Download and install [jamovi](https://www.jamovi.org).
+**Step 1: Download and install [jamovi](https://www.jamovi.org).**  
 
 
-- Step 2: Download the relevant `jmo` file for your operating system from 
+**Step 2: Download the relevant `jmo` file for your operating system from**  
+
+*a: For development version*
 
-    - a: For development version
 
 - [releases](https://github.com/sbalci/ClinicoPathJamoviModule/releases/)
 - [sourceforge](https://sourceforge.net/projects/clinicopathjamovimodule/files/latest/download).
 
-    - b: For stable version
+
+*b: For smaller modules*
+
+
+- ClinicoPath:
+
+
+https://github.com/sbalci/ClinicoPath
+
+
+https://github.com/sbalci/ClinicoPath/releases
+
+
+- JJStatsPlot: 
+
+
+https://github.com/sbalci/jjstatsplot
+
+https://github.com/sbalci/jjstatsplot/releases/
+
+
+*c: For stable version*  
+
+
 
 - windows: https://library.jamovi.org/win64/R3.6.3/ClinicoPath-0.0.2.jmo
 
@@ -84,7 +108,7 @@ Then you can install this module directly inside the jamovi, using library.
 
 
 
-- Step 3: And install using side-load as shown below:
+**Step 3: And install using side-load as shown below:**
 
 
 <img src="man/figures/jamovi-sideload.gif" align="center" width = 75% />